The New Team Rocket
by Kuru0
Summary: With Team Rocket crumbling after Giovanni's embarrassing defeat at the hands of Red, Giovanni's son, Gene, steps up to take the reigns. He dreams of a Team Rocket that will take whatever they want and will do anything to achieve it. Petty crime is no longer Team Rockets focus. Heavy Crime has come to Kanto and Gene is leading it. Murder/Drugs/Theft/Kidnapping and more. M-Rating


**This is going to be a start of a new story I wanted to try out. I call it, The New Team Rocket.**

 **This story is going to be about Gene, Giovanni's son. When Giovanni gives up on Team Rocket after being embarrassed by Red defeating him and his captains, Gene steps in to take the reigns to step Team Rocket up and turn it into a real crime syndicate instead of the weak mentality that it held before.**

 **There are a few names that might be a little odd. First is the rocket executives. They have their english and japanese names, I am just going with what sounded better to me.**

 **Giovanni had a son, yes I know. His son was the rival in the second gen games. I am doing things way different and using some actual things that happened and making up new scenarios.**

 **There are other bits of his back story that I am changing, if something seems off don't worry, I will adjust or explain it further down the line.**

 **This is strictly a secondary story and I will still be focusing on Trust By My Side. I will be working on this as a side project and depending on how well it goes over I will make it longer and longer. It is by no means a one shot so don't worry about that.**

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 **I do not own Pokemon**

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Gene could feel the start of a headache coming on. He had been going through all of the remaining members of Team Rocket after his father gave everything away.

His father, Giovanni, had the ideal that he would take Pokemon away from the trainers and use them for extortion and empty threats. His political power, while substantial, was only political power.

Gene was a bit more of a visionary. He had plans to make Team Rocket a true, criminal, organization.

He had been around Team Rocket for a few years now. Several of the lieutenants had known of him and had respect for the boy. He was only 16 years old and had a true sense for the criminal way of life.

Many of the lower ranking members had lost their nerve after hearing of Gene's plans. They were all in the group when it was for extortion and theft. The odds of getting caught were relatively low at that time.

Gene however, had plans of controlling everything. His first targets were to take over the black markets and recruit some more talent.

Several of the grunts did not want to be involved in taking over the black market and had left. Gene did not press them, he did not care for weaklings anyway.

Finally getting to the highest ranked members he called back from Johto, his four highest ranking members in charge of the entire operation in Johto.

All four of them were now standing before him in his office. He called the first to step forward.

First up was Apollo. Apollo stepped forward and bent down on one knee.

"Apollo, you have been the executive in charge of the Sevii Islands for a long time now. My father trusted you with complete control of that operation and only asked for monthly reports. I will be completely scrapping all operations in Johto so as to focus on Kanto." Gene started. He kept a close eye on the members in front of him to see any weakness.

"Here in Kanto, we will be doing things a bit more, excessively. I will need you to continue research. Our theft of pokemon will be increased so there will be far less restrictions on what you can do. If you show results, any failures will be forgotten. A lab is being built as we speak and should be operational in less than a months time." Gene said with a pause.

"Until then, you will be overseeing the lower ranked members adaptation to new management and training of new recruits. I will find you a new person to train as a trainer so it will not be a permanent station. Will you accept these charges and swear your loyalty to myself and Team Rocked as a whole once again?" Gene said as he eyed Apollo.

Apollo leaned forward to bow from his kneeling position. "Of course sir." Apollo replied before getting a nod from Gene to stand back up and rejoin the ranks.

The next member stepped forward and went down on one of her knees.

"Athena, you have been the executive in charge of our warehouses since they have been built in Johto. Here in Kanto, we will need an overseer for our warehouses. These warehouses will be holding far more than stolen pokemon and small time narcotics. They will be filled with stolen pokemon, high end drugs, weapons, and anything else we acquire. I will trust that anything that may come through our warehouses will be properly cared for and guarded. Will you accept these charges and swear your loyalty to myself and Team Rocket as a whole once again?" Gene asked with authority.

Athena bowed lower and said. "Yes sir."

Gene could hear the confidence in her voice and told her to rejoin the ranks.

The third executive stepped forward and took a knee.

"Petrel, you were tasked as a master of disguise. Your skills allowed you be work your way through many security systems and your charms allowed you to gain the trust of many corporate executives in Johto. You will be moving between corporation to corporation to build trust with them and increase our influence. You will also get an ear into the police higher ups to feed us info on how much the police are focusing on us. Will you accept these charges and swear your loyalty to myself and Team Rocked as a whole once again?" Gene asked yet again.

Petrel bowed his head. "Yes sir."

Gene was in a good mood after hearing that. Petrel would be important moving forward and was relieved to hear him staying. He motioned his to rejoin the ranks and called forth his final executive.

He stepped forward and took a knee in front of Gene.

"Proton, you were in charge of our smuggling operation in Johto. Here in Kanto, we will first take control of the black market. We will force them to bow under our rule or destroy them completely. We will not being pussy-footing around this. If they will not submit or join, burn their operations to the ground and we will rebuild it. We will be smuggling heavy narcotics along with stolen pokemon, weapons and most likely even more. You will be the head of the new black market when all is done. Will you accept this charge and swear your loyalty to myself and Team Rocket as a whole once again?"

Proton smiled and bowed his head. "You didn't even need to ask sir."

Gene smirked at this and nodded to him.

"You all have your assignments, your men will be waiting for you on the second floor. Go to them, tell them of their new assignments and if they wish to leave, kick them out. I will not deal with people that are not 100% devoted to our cause. Message me your total numbers afterwards and we will have another meeting in two hours. My secretary has your new executive uniforms and your orders waiting for you. You are to wear your new uniforms whenever you would wear a normal uniform. Dismissed." Gene said with a wave of his hand.

All four of the executives gave a shout of, "Sir." and a salute before turning on their heels and walking out the door.

Each of their uniforms were different for each of them. They were far more than a basic suits and showed they were upper echelon of Team Rocket.

Apollo and Athena both had their suits with a black under shirt and white over it. Apollo had white formal pants with a short cut white jacket with is Team Rocket symbol where his left, breast pocket would have been.

Athena had a white dress that was slit past her knees with black trim. She also had her symbol over her left breast.

Petrel had a bit more of a classic outfit. He was given a white short sleeved undershirt and an open black, vest. His vest had thin, yellow strips running up the front. He was instructed to keep his boots under his pant legs so as to not draw attention to himself when not needed. His emblem was on his white undershirt.

Proton had a similar outfit as Petrel. His black jacket had his yellow trim along the edges of it instead of just up his chest. He also wore the standard white gloves and boots more openly. His emblem was on his left breast pocket as well. He also kept his grunt hat as a way to seem more relatable to his men.

They gave each other a look over and nodded before addressing their men.

Back in his office, Gene was grinning like a madman. All of his executives were still with him and accepted their new positions.

With how much different Team Rocket was and how heavy the new crimes they would be committing, he expected at least once of them to drop. Keeping all of them would be a good sign and would promote more trust down the lines.

Many of their men had never worked for his father after all. With the same management as before, many more would stay.

He would be going over the last stock reports of the warehouses before they returned in two hours. He needed to know what pokemon he had and which he could control. He would need more of the badges first if he wanted to get absolute control of the pokemon for him and his men.

The badges were curious little things. Most trainers only saw them as a medal of honor. Gene however, saw them as a simple yet effective way to control pokemon.

Many pokemon that had been trained before had at least the notion that the badges meant a strong trainer. There was also the subtle charm to them that made pokemon a bit more receptive to orders.

He would need to gather support of the gyms or even take them over if he wanted to get a stream of them to his men. If only his idiot father had not destroyed his own gym. It would have made things a lot easier for him.

There were also the black markets to take over. Gun laws were very strictly enforced so they were very difficult to obtain. The noise disturbed the local pokemon and after a few cases of people being mauled by pokemon their recreational shooting stirred up, people tended to stop buying guns and the laws got fiercer.

Violent crime had also seen a huge decline in recent years and people were getting to comfortable. Honor and prestige were valued far too much in Gene's opinion. It was a world where fortune came through fame and fame was gotten through straight up 1v1 pokemon battles.

He would violently cast that to the side and take the fortune he wanted. Those that would stand in his way will learn what pokemon are truly capable of.

His father was renowned as one of the greatest pokemon trainers because of his attention to how the pokemon battled and knowing everything he needed to know about his pokemon.

Gene would take it a step further and use that knowledge outside of just battles.

He knew of many poison pokemon that could be used to kill or paralyze wide areas of people. Pokemon that could level entire city blocks if he needed to.

He would go as far as he needed to, no matter the cost. If he had to resort to mass terrorism, he would without hesitating.

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Down stairs, the executives were rallying their men and trying to boost their confidence in their new leader. Most stayed true to their leaders, a few saw the change of management as Team Rocket taking a decline.

Many stayed simply because they would still be taking orders directly from their executives and did not care too much that someone else was in charge of Team Rocket as a whole.

Only around five percent of their men had elected to leave and that was quite good in their books. They started to look at their new orders and started to delegate men to their new tasks.

It would be quite a headache getting used to an entirely new region but they would have to get started soon.

They still had a few hideouts that were not discovered and even fewer that had been out of commission for a while that could be restored.

Currently they were within one of their office buildings on the edge of Saffron City. The town was large enough that they could move a bit more freely and it was not that hard to keep the police at bay since it was a legitimate business being run throughout the building.

It had the added bonus of pulling in a steady stream of profit. Their funds were slowly dwindling with the falling out of Giovanni's political power he had amassed and they needed the extra cash.

Everyone's first priority was to gain control of the black market. Once they had the black market, money would come in and so would new members. Warehouses were also useless without something to put into them.

Most of the nameless grunts had been told to keep a low profile with their robbing of pokemon and even encouraged to catch their own. Many didn't understand why until the executives had told them all the story of how Giovanni was known as one of the strongest trainers to live.

Giovanni had trained his pokemon from the ground up and became fiercely loyal. If he had told them to lay down their lives for him, they would have done so without hesitation.

That seemed to sprout a few questioning gazes when they first said that. Many had been told to see pokemon as tools and nothing more. A means to an end.

Hearing their leader put so much trust in his pokemon before and that their new leader followed the same principles quelled a bit of the uncertainty in some of the men. It showed strong character to some and loyalty to the future in others.

Trainers tended to be fairly well respected by everyone. It took dedication and a good heart to raise a strong pokemon and that was a quality many admired.

Gene was of course far more than just a trainer, he did however earn the same respect as a strong trainer himself.

He had trained with his father when he was still a gym leader. Even is the gym was mostly a cover, the skill required to become a leader was tested rigorously.

Seeing the motivation in the room, the executives tallied up their totals and started to head back to report to Gene's office.

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In his office, Gene was wrapping up his planning. He needed to gather some badges and he needed them in bulk. This of course was impossible by conventional means. It was a good thing Gene was not conventional.

He would need a bit more manpower and he just needed to find the right motivation to get a few people he wanted. Sitting around for two hours while his executives talked to their men gave him more than enough time to think of some talent to recruit.

The night was starting to drag on and he would not bother until the next day. He still needed to finish talking with his executives.

Shortly after thinking about it, he hear a knock at his door. Calling everyone in, his executives once again stood before him.

"Well, how are our numbers looking?" Gene asked getting to the point.

Apollo stepped forward and gave a summary of how many they lost. Five percent wasn't near as many as Gene had expected to drop so he was rather pleased with this.

"Very well. Five percent was to be expected to say the least. Regardless, for now, you all have your orders. First however, I have gotten a report from one of my personal spies that a person I am interested in might be leaving for Johto soon. I would rather recruit him before he leaves. Follow me to basement three, I need to know what your pokemon are capable of." Gene said before getting up and walking toward the door.

"Sir." Everyone said before turning on their heels and following Gene to the elevator. He pulled out a key and turned it into the elevator consol. "With all of the paperwork I have been doing all week, I am rather pleased to stretch my legs again." Gene said suddenly.

Everyone glanced at him to see him smiling as the door finally opened revealing a large, open room that seemed to be reinforced.

"All right lady and gents. This is a training area I had built a few months ago. I am the only one with the key currently. Depending on how well everyone does, you could get a key for your own." Gene said as he walked in.

It was a large room with not much in it. There was a few targets painted on one end of the room and a few wooden dummies.

Otherwise, there was nothing there. Just a large, empty room. "Here, we will have our battles, Obvious rules would be no destroying the ground, no self destructing, try not to flood the place too bad, other than that, anything goes." Gene explained.

The executives nodded, destroying the terrain and possibly sinking the building above them would be rather bad. "So who will be going first?" Apollo asked.

"First? It is a four versus one. Two pokemon each, swap out after they go down. You will be going against Gardevoir and Gallade here." Gene said as he dropped two pokeballs and a Gardevoir and Gallade came out.

"These two, are brother and sister. They have been my partners for the last year now. When I went with Father to visit his old comrades in Hoenn, I caught Gardevoir when she was still a Kirlia. Seeing his sister taken from her home, Gallade evolved and attacked me furiously. When I managed to finally defeat him, I decided to capture him as well." Gene said as he smiled at his pokemon.

"After I healed everyone, I went back and opened their pokeballs. I sat and calmed them down for an hour until Gallade finally settled down. Kirlia warmed up to me and Gallade followed soon after. I tried training Kirlia individually, she never seemed to be into the training until I had her train with Gallade. Together, their teamwork helped push them further than they could have done alone." Gene finished as he started walking back away from them.

"So, who will you all lead. I recommend taking a moment and thinking of a strategy. We will not go easy on your at all. Try to last longer than five minutes." Gene said once more with a smirk.

The executives, all thought a little slowly, walked away and decided to think on a strategy. "So I would think we just rush for the instant win. He is clearly underestimating us thinking he can take all four of at once." Petrel said.

Proton agreed, Apollo however did not. "I think we should go for a slow burn battle. We already know what his pokemon are and if their teamwork is as great as he claims, a quick fight might not work. I think we should try to cover the area with poison and slowly whittle down his pokemon."

Athena agreed instantly and Proton and Petrel came around after they discussed their pokemon around. Focusing on wide spread poison and attacks of opportunity were their only option.

They turned around after their discussion and faced Gene. Gene smirked at them. "You seem to have a plan, good. One last thing I should mention. This will not be a honor filled battle. My pokemon have been told to hold back and not kill your pokemon. They will not follow through on a death blow but if I see it, I will call it out and you will return that pokemon to their ball at once. Am I clear?" Gene said with a commanding tone.

"Yes sir." Everyone replied. "Good, shall we being?" Gene said as he stepped back to get out of the fight.

Everyone nodded and pulled out their first ball. "Go, Houndoom/Arbok/Koffing/Weezing." They all cried out as they tossed their pokeballs into the field.

Gene smirked at them, he could tell what they were doing. He would not give them the chance to even try it however.

"Gardevoir, Thunder Wave the Arbok. Gallade, X-Scissor it." Gene commanded as soon as the pokeballs opened.

Gardevoir hit Arbok with Thunder Wave and paralyzed it before it get fully out of the ball. Within the second, Gallade was on top of it with X-Scissor. Realizing that they didn't even get enough time to set up all of their planning went to hell instantly.

"Shit, Weezing use Toxic." Proton yelled. "Koffing, Smog." Petrel said. "Houndoom hit him with Flamethrower."

Gene smirked again. So they wanted to go with a slow poison fight. He wouldn't let them however.

"Gardevoir use Light Screen for Gallade. Gallade, switch to the Houndoom with Close Combat. Blow through the flamethrower." Gene called out. Not hesitating, Gallade stepped off of the Arbok and dove straight into the flames. Light Screen came up in front of him before the fire hit and blocked most of the damage.

"Houndoom get out of there." Apollo yelled, but it was too late. Gallade was already on top of Houndoom and was tearing him apart. Gallade was far faster than Koffing and Weezing, not to mention he closed the distance to Houndoom faster than Apollo could give a command.

Everyone was shocked by how fast paced the battle was going and it was a four versus one. There was no time waste in his pokemon's moves and they seemed to have the familiarity between themselves that his pokemon didn't question him at all.

Falling out of their shock when they heard Gene call for his Gardevoir to finish off Arbok with Psychic. Athena barely blinked from where the Gallade have stepped off of her Arbok to when it got blasted with Psychic. She called Arbok back and tossed out her Raticate.

"Raticate, Hyper Fang while his back is turned." She called out. Before she switched, Proton and Petrel called their pokemon to switch their focus onto Gardevoir. Before the attacks even left their pokemon, Gardevoir had dodged.

They how shouted "How!" as their pokemon missed by a long shot. "Gardevoir can see the future. I have trained her to keep dodging without my input. She will not be hit by something far slower than her." Gene said with a smirk.

After he finished explaining to them, the Raticate was almost upon Gallade. "Gallade, catch it and use Fury Cutter. Aim for its whiskers." Gene called out.

Heeding the call, Gallade turned caught the Raticate in mid air with one arm and sliced off half its whiskers with his other arm. Gallade pushed Raticate back and sliced the rest of its whiskers off, causing it to stumble.

"Raticate get out of there!" Athena yelled. "Gallade, Fury Cutter once more." Gene called out at the same time.

Without its whiskers, Raticate proved to not have the balance to run fast enough and was caught by Gallade once again. After two more hits, Raticate was knocked away and crumpled into a heap at Athena's feet.

Checking her pokemon, she saw he was out and called him back to his pokeball and walked away from the fight.

Koffing and Weezing were still chasing Gardevoir, without any success. Seeing a small opportunity however, Apollo called for Houndoom to use Bite on Gallade while his back was turned.

"Gardevoir, Reflect for Gallade. Gallade, catch the Bite with X-Scissor." Gene called out seeing the Houndoom going for a sneak attack.

The Reflect came up a moment after he lunged for Gallade's neck. The Reflect slowed him down enough for Gallade to turn around and catch Houndoom's Bite with a vertical X-Scissor. The result was Houndoom's mouth being held open by Gallade's elbow blades.

"Houndoom is done, if Gallade completed his attack, Houndoom's jaw would have snapped and he would have been crippled most likely permanently. Call him back." Gene ordered.

Seeing his Houndoom unable to clamp down on Gallade's blades, Apollo called him back and sent out his Crobat.

"Crobat, Confuse Ray." Apollo called out as soon as Crobat came out of his ball. Unfortunately, Light Screen was still active and blocked most of it. The result was Gallade got a headache at that was about it.

"Smart, but not smart enough. Gardevoir, hit Crobat with Psychic. Gallade, catch one of its wings with X-Scissor." He commanded.

Before he could call his Crobat to try and dodge, he was blasted with the Psychic and tossed off balance. As soon as he had to flap his wings to try and correct himself, Gallade was already on top of him with his left wing caught by Gallade's crossed elbow blades.

"Crobat is out, in his current position, Gallade could rip a wing off and end the right." Gene called out calmly.

Apollo grinded his teeth and called Crobat back. He walked over to stand next to Athena and talked about how they got completely destroyed instantly.

Gene called out to Petrel and Proton. "With your teammates both out, I believe this has come to an end. You all had one chance in a four versus two match but now that it is even numbers, your strategy is gone."

Both looked to Apollo and Athena and they both nodded to just surrender. They looked at each other and nodded as well and called back their pokemon. Gene started to walk forward and praised his pokemon with a job well done before calling them back to their pokeballs.

Everyone met up in the middle of the room as Gene started talking. "I honestly cannot be too surprise at his outcome. You all have been too comfortable with the relaxed nature of being in charge. The problem with your strategy, was I saw through it instantly and it relied too much on one pokemon."

All four executives nodded grimly at this. They relied too heavily on Arbok being able to paralyze one of the two enemies to get an advantage right off the bat. Without Arbok's paralysis in place, Koffing and Weezing were far too slow to poison either enemy and thus they were swiftly defeated.

"Now then, Apollo, your Houndoom is trained well. He went directly for Gallade's throat and that is good mentality. Train him more and keep him close. Athena, your Arbok and Raticate are far too slow to be effective, work on it. Petrel and Proton, your pokemon excel at wide range poisons and yet you focused on narrow attacks. Teach them to use wide ranged attacks and get pokemon that can slow an enemy down so the poison will hit." Gene said, dissecting their entire teams.

Everyone nodded in understanding and yet Gene continued. "Also, what is the weakness in a battle with trained pokemon?" He asked everyone.

Everyone gave answers along the lines of they are more relaxed or not as vicious.

"While you are all correct, the main weakness is the trainer." He said simply. Seeing everyone have a confused look he continued. "Perhaps a demonstration as to what I mean." Gene suggested.

He pointed to the wooden dummies. "That will be a pokemon trainer." He said as he tossed out a pokeball. "Jolteon, Pin Missile, vitals, go." He commanded as Jolteon was still coming out of her ball.

As soon as Jolteon came out of her ball, her feet touched the ground and instantly there were lightning charged missiles in the air. They hit the dummy where each eye would be, two in the throat, three through where its heart would be , two through where each lung was, and then finally four more in a line across the stomach.

Gene called Jolteon over to him and gave her the praise due. As Gene sat on the floor to pet his Jolteon, the executives quirked an eyebrow at the behavior. In general, a Jolteon tended to constantly push out enough static to seriously hurt a person. Yet here was Gene practically cuddling with one.

Gene finally spoke up after a moment. "Now then, with the trainer in that condition, what would be stronger, a wild pokemon, or a trained pokemon?"

They all agreed that a wild pokemon would be stronger as a trained pokemon would be frozen after seeing their trainer killed and would not have anyone to give it a command.

"Exactly. This is how my Team Rocket will operate. If you are in the eye of the public, fight to defeat the enemy and embarrass them. In the shadows, if you cannot win quickly, kill or main the trainer depending on the situation." Gene said with a commanding tone.

The executives were starting to understand how Gene destroyed them so easily with only two pokemon. They were aiming to just blindly hit his pokemon. He trained his pokemon to target weak points and break them down without putting up a fight.

"You will each train your pokemon to fight as if it were life or death. A crippled pokemon poses little threat while a dead one will never be a threat again." He said while he motioned for his Jolteon to follow him to the elevator.

"Come, we must get your pokemon restored and then go visit an old friend of mine in Fuchsia City." Gene said as he stepped into the elevator.

"You will all get a key to come to this floor soon enough. I expect you to use it whenever you have the time. I want to see results soon." He said as the elevator doors closed behind them.

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 **Ok, that is a wrap on Chapter 1. Got the executives introduced and I feel I got a fair representation on how I will be doing this story out there.**

 **I will say it again before anyone coming from my other story, Trust By My Side, freaks out. This is my second story and as such is second on my priority list. I hope to get a chapter of this out after every chapter or my main story but there is no way to tell if that will be the case yet.**

 **I tend to work on this whenever I hit writers block on my main story so when I work on this has been erratic. Now that I have a chapter posted however, it gives me more reason to work on it. Instead of just pretty much writing notes for a story I want to do, it is now continuing a story I have written.**

 **Let me know what you think and if you want to talk to me in a Kik chat, I am still in #TrustByMySide and will probably build a new chat for specifically this story if I get enough people that would want to join.**

 **With that, I will see you all in the next chapter, thanks for reading.**


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